[gmx-users] Constraints - again

[David van der Spoel]

On Thu, 2004-12-16 at 08:46 +0100, Uwe Richter wrote:
> Thanks for the reply,
> 
> Distance restraints won't to the job I suppose, since I'd need a
> second atom to which
> the restraint refers to. I just do not want the atoms of the loop to
> move too far from the
> current position, say only +/- 2 angstrom in all dimensions. Amber
> provides such a
> feature but I don't know if it is possible to achieve this with
> Gromacs. 
> I have tried to define a set of atoms at exactly the same position as
> the loop atoms,
> didn't define any bonds, pairs etc. for them, gave them zero charges
> and applied position
> restraints. To these atoms I defined distance restraints for my real
> atoms, however,
> the minimizations/simulations crashed. Is this procedure in general
> possible and I
> did something wrong in the set up? If not, is there another, may be
> easier way
> to do it?
Nice idea, I don't see why it wouldn't work, except when they still
would have Lennard Jones interaction. 

Otherwise position restraints is your only option. If you feel like
coding a bit (src/gmxlib/bondfree.c) you could modify the position
restraint algorithm such that it implements the hard-wall type restraint
that you want.


> 
> Thanks again,
> Uwe
> 
> David van der Spoel wrote:
> > On Wed, 2004-12-15 at 12:53 +0100, Uwe Richter wrote:
> > > Dear all,
> > > 
> > > is there a way to let parts of a protein move only a certain
> > > distance from the current position. I have a loop and I want
> > > to relax it by high temperature MD or simulated annealing but
> > > I don't want it to move too far away.
> > Use distance restraints (not these are not constraints)
> > > Thanks for you help,
> > > Uwe
> > > 
> > > 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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